chr20-7838574-C-T

Variant names:

• chr20-7838574-C-T
• rs2423291

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.286 in 151,948 control chromosomes in the GnomAD database, including 6,525 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.29 (6525 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.47 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43454 AN: 151830 Hom.: 6502 Cov.: 33

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.304

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.286 AC: 43523 AN: 151948 Hom.: 6525 Cov.: 33 AF XY: 0.286 AC XY: 21266 AN XY: 74280

African (AFR) AF: 0.329 AC: 13646 AN: 41438

American (AMR) AF: 0.303 AC: 4628 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.338 AC: 1173 AN: 3468

East Asian (EAS) AF: 0.327 AC: 1691 AN: 5178

South Asian (SAS) AF: 0.487 AC: 2345 AN: 4820

European-Finnish (FIN) AF: 0.206 AC: 2169 AN: 10554

Middle Eastern (MID) AF: 0.298 AC: 87 AN: 292

European-Non Finnish (NFE) AF: 0.248 AC: 16872 AN: 67922

Other (OTH) AF: 0.312 AC: 659 AN: 2114

Alfa AF: 0.144 Hom.: 264

Bravo AF: 0.294

Asia WGS AF: 0.444 AC: 1538 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.21
DANN	Benign	0.36
PhyloP100		-1.6

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2423291; hg19: chr20-7819221;